User: Vitis

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Vitis2.3k
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A plant geneticist from a taxonomist and naturalist background. Now trying to bridge classic genetics and evolutionary biology with ever-expanding genomic data and bioinformatic tools.

Posts by Vitis

<prev • 328 results • page 1 of 33 • next >
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Variant calling from short/long read hybrid BAM
... Is there an approach that takes in a hybrid BAM that contains both short and long reads and call variants, especially bigger structural variants? I think it will be more common to have both long and short reads for a genomic region. A variant caller that takes advantage of the hybrid data may be val ...
snp sequencing written 13 hours ago by Vitis2.3k
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Answer: A: Circos Plot for synteny file
... On way to do this is to lay out the chromosomes from two genomes into left and right panels, then draw connections/links based on synteny relationships between chromosomes across genomes. See Fig. 2 from the Canola genome paper published in 2014. https://science.sciencemag.org/content/345/6199/950 ...
written 3 months ago by Vitis2.3k
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Answer: A: How are haplotypes/heterozygosity resolved in sequence assembly?
... I think the ultimate goal for assembling a heterozygous genome is to fully resolve the two haplotypes, essentially two genome assemblies. Platanus seems to be doing a fairly job dealing with heterozygous genomes. Also, long-read sequencing technologies like Nanopore and PacBio would enable variant p ...
written 3 months ago by Vitis2.3k
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Answer: A: A good tutorial for eukaryotic phylogeny?
... I came across this paper recently about reconstruction of genome phylogeny for a butterfly species radiation. The methodology might be interesting for you to take a look. They used long reads assembled genomic sequences and Cactus to align the genomes, then created gene trees and species trees, etc. ...
written 3 months ago by Vitis2.3k
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Answer: A: BWA Mem -M flag (mark split hits) effect on structural variation calling
... I've never used -M option for structural variant calling. Based on this BWA thread, you may lose supplementary mapping information by using -M option, because -M may label split reads as duplicates and strip the secondary/supplementary mapping information. I believe at least some SV tools use split ...
written 4 months ago by Vitis2.3k
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Answer: A: Variant Annotation and prioritization
... The annotation tools snpEff would be a good start. You may also look at PyVCF to extract genotypes from VCF files. http://snpeff.sourceforge.net https://pyvcf.readthedocs.io/en/latest/ ...
written 5 months ago by Vitis2.3k
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Comment: C: Mutant Transcript is higher than the WT. What may be the reason?
... One simple way to try this is: for each sample, count total number of reads mapped within the gene boundaries, divide by the number of total reads, then multiply 1 million. This gives you the reads/million for this gene in this sample, so you can compare this value across samples. Basically, for eac ...
written 5 months ago by Vitis2.3k
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Comment: C: snpEff build not working with gff3
... For GFF3 annotations downloaded from Ensembl (which should meet all GFF3 standard and pass GFF3 validations), I used "-gtf22" option instead of "-gff3" and it worked fine in snpEff. ...
written 5 months ago by Vitis2.3k
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Answer: A: Visualizations of chimeric connections in different chromosomes
... I'd suggest querying the alignments and find inter-chromosomal chimeric connections and visualize them with circos. It is possible to visualize intra-chromosomal connections within the same framework. And the unusual ones, if those are what you're after, would stand out in circos plots. http://cir ...
written 5 months ago by Vitis2.3k
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Comment: C: Mutant Transcript is higher than the WT. What may be the reason?
... Comparing expression levels from IGV views is not very informative. You need to at least normalize against library size to compare expression levels of a genes across samples. ...
written 5 months ago by Vitis2.3k

Latest awards to Vitis

Scholar 3 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Voter 4 months ago, voted more than 100 times.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Scholar 12 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 12 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 14 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Scholar 15 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 17 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 17 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Great Question 3.2 years ago, created a question with more than 5,000 views. For Mapping Rates From Bwa
Good Answer 3.2 years ago, created an answer that was upvoted at least 5 times. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Scholar 3.2 years ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Appreciated 4.8 years ago, created a post with more than 5 votes. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Appreciated 4.8 years ago, created a post with more than 5 votes. For A: How To Convert Centimorgan To Base Pair
Good Answer 4.8 years ago, created an answer that was upvoted at least 5 times. For A: A Result From Mummer Alignment
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Housekeeping Gene Identifications
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Mapping Rates From Bwa
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler
Guru 6.0 years ago, received more than 100 upvotes.
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Supporter 6.0 years ago, voted at least 25 times.

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